Abstract Inflammatory bowel diseases (IBD) represent a spectrum of complicated intestinal pathology characterized by dysregulation of the adaptive and innate immune responses in genetically susceptible hosts. The precise molecular mechanisms underlying the pathophysiology and immune dysregulation have yet to be fully elucidated. A significant barrier to better understanding of the disease pathogenesis is the heterogeneity of intestinal tissue. Furthermore, substantial heterogeneity may exist even within the same phenotypic cell subset, limiting the ability to detect differences using bulk RNA sequencing or flow cytometry. Single cell RNA sequencing and single cell protein identification in combination, however, represent a significant technologic advance with the capability to identify novel cell subsets and states that could not be previously detected. We propose exploiting this technology to generate a single cell atlas of the intestinal and peripheral blood immune response in two subsets of IBD: ulcerative colitis (UC) and ileal Crohn?s disease. The overall objective of this proposal is to define molecular determinants of IBD in tissue and blood, then to harness these differences in gene expression to develop novel diagnostic testing for IBD using peripheral blood. Specific Aim 1 proposes to identify abnormal states of differentiation and pathogenic cell subtypes that are enriched in the intestinal tissue and peripheral blood from UC and Crohn?s ileitis as compared to healthy controls. The differences in gene expression between the intestinal cells from IBD patients and healthy controls will provide insight into molecular determinants of disease that are specific to UC and Crohn?s ileitis. Specific Aim 2 proposes to utilize the differences in single cell gene expression from the peripheral blood in a larger cohort of patients to develop diagnostic testing for UC and Crohn?s ileitis. Non-invasive testing with single cell gene expression has the potential to predict not only disease status but also severity of disease activity with potential therapeutic targets. In sum, this proposal aims to use single cell gene and protein expression to understand disease pathophysiology of IBD and develop novel diagnostic biomarkers.